Methods for determining carrier status

Abstract

The invention generally relates to methods for determining carrier status with respect to a condition or disease. In certain embodiments, the method involves exposing a sample to a plurality of molecular inversion probes capable of capturing DNA from at least one genomic region suspected of having an altered copy number and at least one internal control DNA known or suspected to have a stable copy number, capturing and sequencing DNA that binds to the molecular inversion probes, and determining a copy number state of the at least one genomic region based on the sequence results.

What is claimed is: 
     
       1. A method for determining copy number, the method comprising:
 obtaining a sample from a patient, the sample comprising genomic DNA that includes a genomic region suspected of having an altered copy number and an internal control DNA having a stable copy number; 
 fragmenting the genomic DNA to yield target nucleic acid comprising fragments of the genomic region and fragments of the internal control DNA; 
 providing a plurality of molecular inversion probes capable of capturing the fragments of the genomic region and the fragments of the internal control DNA; 
 exposing the target nucleic acid to the plurality of molecular inversion probes; 
 capturing DNA that binds said molecular inversion probes; 
 sequencing the captured DNA to produce target sequence reads and control sequence reads; 
 enumerating target read counts from the target sequence reads and control read counts from the control sequence reads; 
 normalizing the target read counts with respect to the control read counts; 
 comparing the normalized target read counts to normalized read counts for a control diploid locus; and 
 determining a copy number state of the genomic region; 
 wherein one or more of the enumerating, normalizing, comparing, and determining steps is performed using a computer system comprising a processor couple to a memory. 
 
     
     
       2. The method of  claim 1 , wherein said determining step comprises determining differences between the normalized target read counts and the normalized read counts for the control diploid locus based upon the comparison. 
     
     
       3. The method of  claim 1 , wherein the normalized read counts for the control diploid locus are obtained from a control sample that is different from the sample. 
     
     
       4. The method of  claim 3 , wherein the normalized read counts for the control diploid locus are obtained from a synthetic nucleic acid in the control sample. 
     
     
       5. The method of  claim 1 , wherein the genomic region comprises a first gene and a second gene, wherein the first and second genes are homologs, orthologs, or paralogs. 
     
     
       6. The method of  claim 5 , wherein the first gene is SMN1 and the second gene is SMN2. 
     
     
       7. The method of  claim 6 , further comprising the step of diagnosing a carrier phenotype for spinal muscular atrophy. 
     
     
       8. The method of  claim 1 , wherein the sequencing step comprises a next-generation sequencing method. 
     
     
       9. The method of  claim 1 , wherein the determining step comprises determining a difference between the copy number state of the genomic region and a copy number distribution encompassing a plurality of stable control loci. 
     
     
       10. The method of  claim 1 , wherein the sample is blood. 
     
     
       11. A method of determining copy number between two paralogous genes, the method comprising the steps of:
 obtaining a sample from a patient, the sample comprising genomic DNA that includes a first gene, a second gene, and an internal control genetic locus, wherein the first gene and the second gene are paralogs; 
 fragmenting the genomic DNA to yield target nucleic acid comprising fragments of the first gene, the second gene, and the internal control genetic locus; 
 providing a plurality of molecular inversion probes capable of capturing the fragments of the first gene, the second gene, and the internal control genetic locus; 
 exposing the target nucleic acid to the plurality of molecular inversion probes; 
 capturing DNA that hybridizes to one or more of the plurality of molecular inversion probes; 
 sequencing the DNA; 
 enumerating read counts from the sequenced DNA; 
 normalizing the read counts for each of the first gene and the second gene with respect to the internal control genetic locus; 
 comparing normalized read counts for each of the first gene and the second gene to normalized read counts for a control sample with a known number of copies of the first gene and the second gene; and 
 determining relative copy number of the first gene and the second gene based upon the comparing step; 
 wherein one or more of the enumerating, normalizing, comparing, and determining steps is performed using a computer system comprising a processor couple to a memory. 
 
     
     
       12. The method of  claim 11 , wherein the first gene is SMN1 and the second gene is SMN2. 
     
     
       13. The method of  claim 11 , wherein the internal control genetic locus has a stable copy number. 
     
     
       14. The method of  claim 11 , further comprising reporting carrier status for one or more conditions. 
     
     
       15. The method of  claim 11 , further comprising determining carrier status for spinal muscular atrophy. 
     
     
       16. The method of  claim 15 , further comprising determining carrier status for at least one other autosomal recessive trait. 
     
     
       17. The method of  claim 16 , wherein the at least one other autosomal recessive trait is selected from cystic fibrosis, sickle cell anemia, Tay-Sachs disease, familial hyperinsulinism, Canavan Disease, Maple Syrup Urine Disease, Bloom's Syndrome, Usher Syndrome type IIIA, dihydrolipoamide dehydrogenase deficiency, Fanconi anemia group C, familial dysautonomia, Mucolipidosis Type IV, Usher Syndrome Type IV, Nieman-Pick disease type A/B, Walker Warburg syndrome, and Joubert Syndrome.